Hi
I have 2 questions about rmsd calculation:
1) why rmsd calculation is done on heavy atoms?
2) what means of mass weighted superposition (rmsd is calculated after mass
weighted superposition)
Any help will highly appreciated!
--
gmx-users mailing listgmx-users@gromacs.org
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Hi Lin,
First of all, I would suggest sticking to a single processor until you
have a protocol that works.
Previously you had an issue with the addition of ions to your .top
file. In your protocol, it's not mentioned. Have you made sure that
issue is cleared?
Cheers,
Tsjerk
On Sun, Jan 10, 2010
Hello Gromacs Users,
I would like to run a simulation of a trimer in a DPPC membrane. I
really like the elegant solution that inflategro script offers,
however I'm afraid I won't be able to use it, because I need to have
lipids in a small space between the monomers right in the center of
the box a
Hi
what command is useful for obtaining time-average structure?
Any help will highly appreciated!
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Please search the archive at http://www.gromacs.org/search before posting!
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Hi
I want to obtain interaction energy between protein and dna in simulation
pr-dna complex.
what command is suitable for that?
Any help will highly appreciated!
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Please search the archive at
On 1/10/10 3:51 AM, leila karami wrote:
Hi
I have 2 questions about rmsd calculation:
1) why rmsd calculation is done on heavy atoms?
You calculate RMSD on whatever subset of atoms you wish; you are not necessarily
limited to heavy atoms only.
2) what means of mass weighted superposition
On 1/10/10 7:40 AM, leila karami wrote:
Hi
I want to obtain interaction energy between protein and dna in
simulation pr-dna complex.
what command is suitable for that?
Please read about energygrps in the manual.
-Justin
Any help will highly appreciated!
--
=
On 1/10/10 6:56 AM, leila karami wrote:
Hi
what command is useful for obtaining time-average structure?
Something like g_cluster might do the trick, but be advised:
http://www.gromacs.org/Documentation/Terminology/Average_Structure
-Justin
Any help will highly appreciated!
--
On 1/10/10 5:17 AM, KM wrote:
Hello Gromacs Users,
I would like to run a simulation of a trimer in a DPPC membrane. I
really like the elegant solution that inflategro script offers,
however I'm afraid I won't be able to use it, because I need to have
lipids in a small space between the monomer
leila karami wrote:
Hi
I have 2 questions about rmsd calculation:
1) why rmsd calculation is done on heavy atoms?
2) what means of mass weighted superposition (rmsd is calculated after
mass weighted superposition)
Consider the difference between centre of mass and center of geometry...
Try the doughnut mode in the newest version of the program -- it's
meant for exactly this situation.
http://www.csb.bit.uni-bonn.de/inflategro.html
-- original message --
Hello Gromacs Users,
I would like to run a simulation of a trimer in a DPPC membrane. I
really like the elegant solution
Hi,
the new inflategro with the 'doughnut mode'
(http://www.csb.bit.uni-bonn.de/inflategro.html) might do what you want.
Ciao,
Patrick
Justin A. Lemkul a écrit :
On 1/10/10 5:17 AM, KM wrote:
Hello Gromacs Users,
I would like to run a simulation of a trimer in a DPPC membrane. I
really like
Dear GMX-Users,
I'm testing my 256 full hydrated lipid on blue gene. The purpose is to find out
the right number for "-npme", as mdrun can not estimate itself successfully.
I met the problem that how to match the maxinum allowed number for DD cells
with large number of CPU cores.
My simulation
Hello Justin,
Should I add dum_opls no. in atom type file in which Lennard-jones
parameters will set to zero.
OR.
I don't have to modify anything prog.will take care of lennard-jones
interactions. I have put charge zero on all atom in TYPE B.
Nilesh
On Sun, January 3, 2010 12:57 pm, Justin A. Lem
On 1/10/10 1:03 PM, Nilesh Dhumal wrote:
Hello Justin,
Should I add dum_opls no. in atom type file in which Lennard-jones
parameters will set to zero.
OR.
I don't have to modify anything prog.will take care of lennard-jones
interactions. I have put charge zero on all atom in TYPE B.
You shou
Thank you!
This is what I need, however I keep getting a lot of errors about
uninitialized values. When the script finishes, the membrane is
rescaled, but the protein is untouched in the corner of the new box :(
I'll try to investigate a little bit despite I don't know perl,
however I believe that
OK, now it works. :)
Chris
W dniu 10 stycznia 2010 20:06 użytkownik KM napisał:
> Thank you!
> This is what I need, however I keep getting a lot of errors about
> uninitialized values. When the script finishes, the membrane is
> rescaled, but the protein is untouched in the corner of the new box
I am trying to get this workflow opperational. However, my systems are
getting unstable. I have preped two mdp files: 1) one for restrained 2)
unrestrained. LINCS errors appear for restrained and unrestrained has
infinite energy appearing.
http://boinc.drugdiscoveryathome.com/*em_restrained_rcs_md
On 1/10/10 5:18 PM, Jack Shultz wrote:
I am trying to get this workflow opperational. However, my systems are
getting unstable. I have preped two mdp files: 1) one for restrained 2)
unrestrained. LINCS errors appear for restrained and unrestrained has
infinite energy appearing.
http://boinc.dru
Hello,
I would like to simulate bacteriorhodopsin embedded into a membrane. I
think ffG53a6 is a good choice - force field is quite new (at least
newer than ffgmx) and there are topologies available for the most
popular lipids, for example the set developed by Andreas Kukol.
To run a simulation I
On 1/10/10 6:16 PM, KM wrote:
Hello,
I would like to simulate bacteriorhodopsin embedded into a membrane. I
think ffG53a6 is a good choice - force field is quite new (at least
newer than ffgmx) and there are topologies available for the most
popular lipids, for example the set developed by And
Thanks Justin,
I am not setting any Lennard-Jones parameters to zero for part B. I put
zero charge on all atoms for Part B. (Lennard Jones parameters for B are
same as Part A).
I am using default parameters for "couple-lambda0" and "couple-lambda1".
For one of my simulation (glucose + ionic liq
Chao Zhang wrote:
Dear GMX-Users,
I'm testing my 256 full hydrated lipid on blue gene. The purpose is to find out the right
number for "-npme", as mdrun can not estimate itself successfully.
I met the problem that how to match the maxinum allowed number for DD cells
with large number of CPU c
On 1/10/10 7:02 PM, Nilesh Dhumal wrote:
Thanks Justin,
I am not setting any Lennard-Jones parameters to zero for part B. I put
zero charge on all atoms for Part B. (Lennard Jones parameters for B are
same as Part A).
Under Gromacs 4.0.x, you should be able to leave the topology alone entire
Justin,
Here I have pasted the data about free energy from mdout.mdp file
; Free energy control stuff
free_energy = yes
init_lambda = 0.20
delta-lambda = 0
sc-alpha = 0.6
sc_power = 1
sc-sigma = 0.3
couple-moltyp
On 1/10/10 7:53 PM, Nilesh Dhumal wrote:
Justin,
Here I have pasted the data about free energy from mdout.mdp file
; Free energy control stuff
free_energy = yes
init_lambda = 0.20
delta-lambda = 0
sc-alpha = 0.6
sc_power = 1
Thanks Justin,
I went back to the original pdb files. These were conformations of the same
protein derived from molecular dynamics simulations performed by Andrey.
What I intially attempted was preping the structures using tleap, hoping to
paint in missing atoms for residues. Then use this to rep
On 1/10/10 9:47 PM, Jack Shultz wrote:
Thanks Justin,
I went back to the original pdb files. These were conformations of the
same protein derived from molecular dynamics simulations performed by
Andrey.
What I intially attempted was preping the structures using tleap, hoping
to paint in missing
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